Closes #221 #222 #231 - remove renv, update PR template, remove non-a…

…scii chars (#233)

* #221 remove renv

* #222 updated PR template

* #231 remove non-ascii chars

.Rbuildignore

@@ -1,5 +1,3 @@
-^renv$
-^renv\.lock$
 ^.*\.Rproj$
 ^.*\.lycheeignore$
 ^\.Rproj\.user$

.github/pull_request_template.md

@@ -1,18 +1,18 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.
+Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral family codebase remains robust and consistent.
 
 Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `main` branch until you have checked off each task.
 
-- [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
-- [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
-- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html)
+- [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update).
+- [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files.
+- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
 - [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
-- [ ] Update to all relevant roxygen headers and examples.
-- [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
+- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions]
+- [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately.
 - [ ] Address any updates needed for vignettes and/or templates
-- [ ] Update `NEWS.md` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
+- [ ] Update `NEWS.md` under the header `# admiralophtha (development version)` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
 - [ ] Build admiralophtha site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiralophtha/reference/index.html)" page.
-- [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
-- [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`
+- [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`.
+- [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`.
 - [ ] Link the issue so that it closes after successful merging.
 - [ ] Address all merge conflicts and resolve appropriately.
 - [ ] Pat yourself on the back for a job well done! Much love to your accomplishment!

LICENSE.md

@@ -8,55 +8,55 @@ _&lt;<http://www.apache.org/licenses/>&gt;_
 
 #### 1. Definitions
 
-“License” shall mean the terms and conditions for use, reproduction, and
+"License" shall mean the terms and conditions for use, reproduction, and
 distribution as defined by Sections 1 through 9 of this document.
 
-“Licensor” shall mean the copyright owner or entity authorized by the copyright
+"Licensor" shall mean the copyright owner or entity authorized by the copyright
 owner that is granting the License.
 
-“Legal Entity” shall mean the union of the acting entity and all other entities
+"Legal Entity" shall mean the union of the acting entity and all other entities
 that control, are controlled by, or are under common control with that entity.
-For the purposes of this definition, “control” means **(i)** the power, direct or
+For the purposes of this definition, "control" means **(i)** the power, direct or
 indirect, to cause the direction or management of such entity, whether by
 contract or otherwise, or **(ii)** ownership of fifty percent (50%) or more of the
 outstanding shares, or **(iii)** beneficial ownership of such entity.
 
-“You” (or “Your”) shall mean an individual or Legal Entity exercising
+"You" (or "Your") shall mean an individual or Legal Entity exercising
 permissions granted by this License.
 
-“Source” form shall mean the preferred form for making modifications, including
+"Source" form shall mean the preferred form for making modifications, including
 but not limited to software source code, documentation source, and configuration
 files.
 
-“Object” form shall mean any form resulting from mechanical transformation or
+"Object" form shall mean any form resulting from mechanical transformation or
 translation of a Source form, including but not limited to compiled object code,
 generated documentation, and conversions to other media types.
 
-“Work” shall mean the work of authorship, whether in Source or Object form, made
+"Work" shall mean the work of authorship, whether in Source or Object form, made
 available under the License, as indicated by a copyright notice that is included
 in or attached to the work (an example is provided in the Appendix below).
 
-“Derivative Works” shall mean any work, whether in Source or Object form, that
+"Derivative Works" shall mean any work, whether in Source or Object form, that
 is based on (or derived from) the Work and for which the editorial revisions,
 annotations, elaborations, or other modifications represent, as a whole, an
 original work of authorship. For the purposes of this License, Derivative Works
 shall not include works that remain separable from, or merely link (or bind by
 name) to the interfaces of, the Work and Derivative Works thereof.
 
-“Contribution” shall mean any work of authorship, including the original version
+"Contribution" shall mean any work of authorship, including the original version
 of the Work and any modifications or additions to that Work or Derivative Works
 thereof, that is intentionally submitted to Licensor for inclusion in the Work
 by the copyright owner or by an individual or Legal Entity authorized to submit
 on behalf of the copyright owner. For the purposes of this definition,
-“submitted” means any form of electronic, verbal, or written communication sent
+"submitted" means any form of electronic, verbal, or written communication sent
 to the Licensor or its representatives, including but not limited to
 communication on electronic mailing lists, source code control systems, and
 issue tracking systems that are managed by, or on behalf of, the Licensor for
 the purpose of discussing and improving the Work, but excluding communication
 that is conspicuously marked or otherwise designated in writing by the copyright
-owner as “Not a Contribution.”
+owner as "Not a Contribution."
 
-“Contributor” shall mean Licensor and any individual or Legal Entity on behalf
+"Contributor" shall mean Licensor and any individual or Legal Entity on behalf
 of whom a Contribution has been received by Licensor and subsequently
 incorporated within the Work.
 
@@ -97,7 +97,7 @@ changed the files; and
 all copyright, patent, trademark, and attribution notices from the Source form
 of the Work, excluding those notices that do not pertain to any part of the
 Derivative Works; and
-* **(d)** If the Work includes a “NOTICE” text file as part of its distribution, then any
+* **(d)** If the Work includes a "NOTICE" text file as part of its distribution, then any
 Derivative Works that You distribute must include a readable copy of the
 attribution notices contained within such NOTICE file, excluding those notices
 that do not pertain to any part of the Derivative Works, in at least one of the
@@ -136,7 +136,7 @@ reproducing the content of the NOTICE file.
 #### 7. Disclaimer of Warranty
 
 Unless required by applicable law or agreed to in writing, Licensor provides the
-Work (and each Contributor provides its Contributions) on an “AS IS” BASIS,
+Work (and each Contributor provides its Contributions) on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied,
 including, without limitation, any warranties or conditions of TITLE,
 NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are
@@ -176,7 +176,7 @@ notice, with the fields enclosed by brackets `[]` replaced with your own
 identifying information. (Don't include the brackets!) The text should be
 enclosed in the appropriate comment syntax for the file format. We also
 recommend that a file or class name and description of purpose be included on
-the same “printed page” as the copyright notice for easier identification within
+the same "printed page" as the copyright notice for easier identification within
 third-party archives.
 
     Copyright 2021 F. Hoffmann-La Roche AG and GlaxoSmithKline LLC

R/convert_etdrs_to_logmar.R

@@ -9,7 +9,7 @@
 #'
 #' Source for conversion formula:
 #' Beck, R.W., et al. A computerized method of visual acuity testing.
-#' American Journal of Ophthalmology, 135(2), pp.194–205.
+#' American Journal of Ophthalmology, 135(2), pp.194-205.
 #' doi:https://doi.org/10.1016/s0002-9394(02)01825-1.
 #'
 #' @author Rachel Linacre

R/convert_logmar_to_etdrs.R

@@ -9,7 +9,7 @@
 #'
 #' Source for conversion formula:
 #' Beck, R.W., et al. A computerized method of visual acuity testing.
-#' American Journal of Ophthalmology, 135(2), pp.194–205.
+#' American Journal of Ophthalmology, 135(2), pp.194-205.
 #' doi:https://doi.org/10.1016/s0002-9394(02)01825-1.
 #'
 #' @author Nandini R Thampi

README.md

@@ -42,7 +42,7 @@ remotes::install_github("pharmaverse/admiralophtha", ref = "devel")
 
 ## R Versions
 
-Here’s a summary of our strategy for this package related to R versions:
+Here's a summary of our strategy for this package related to R versions:
 
 * R versions for developers and users will follow the same as
   `{admiral}` core package.
@@ -58,7 +58,7 @@ developer community:
 
 * [Slack](https://pharmaverse.slack.com/) - for
   informal discussions, Q\&A and building our user community. If you
-  don’t have access, use this
+  don't have access, use this
   [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A)
   to join the pharmaverse Slack workspace
 * [GitHub

inst/WORDLIST

@@ -41,7 +41,7 @@ Onboarding
 README
 SDTM
 TAs
-Template’
+Template'
 USUBJIDs
 adae
 adam
@@ -58,7 +58,6 @@ https
 onboarding
 paramcds
 pharmaverse
-renv
 repo
 studyeye
 tribble